Students and Research - SYE 2023/2024
Melinda Barath, Advisor: Dr. N. Marano
Isolation of Amyloid Proteins in Biofilms from Microbacterium Oxydans
When not found in their single cell state, bacteria can be found in aggregate communities, known as biofilms, which are typically attached to a surface, inside or outside the body. Bacteria employ many different families of proteins and other macromolecules in general to promote and maintain biofilm growth, which serves to provide protection for the bacterial colony, making it more difficult for antimicrobial products, for instance, to penetrate, decreasing its effectiveness. Amyloid proteins are one example, which are involved in establishing the foundation for biofilms and provide further protection for the aggregate colony. As a secondary structure, they can form beta-pleated sheets upon folding. Isolated by St. Lawrence students from a pig farm in upstate New York, Microbacterium oxydans has been found to form biofilms and contain amyloids. Students were able to develop an isolation procedure to extract the proteins of interest from biofilms, which is now being studied to improve yield. More specifically, it is necessary to detach these amyloid fibers from the cells, and this can be accomplished using different sonication procedures, as well as the addition of lysozyme to hydrolyze the bacterial cell wall. Depending on the results of these experiments, additional measures, such as adding DNase or detergent, can be taken to conserve the structure of the proteins. Understanding the conditions that are required to isolate the proteins of interest from the microorganisms would increase the amount isolated, thus allowing for further study of how they function, not only in M. oxydans, but also potentially in humans.
Leah Biwot, Advisor: Dr. S. Glazier, Dr. S. Tartakoff
Synthesis and Study of Acridine Derivatives as Potential Chemotherapeutic Agents
Acridine dyes are commonly used for DNA-drug interaction studies because their polycyclic, planar, and aromatic structures can intercalate between adjacent DNA bases, stopping transcription and serving as potential chemotherapeutic agents. In my research, I have prepared a number of acridine derivatives to better understand DNA-ligand interactions and structure-activity relationships. These derivatives were prepared using two approaches: (1) by directly modifying proflavine with various reactions (e.g., amine acylation and aromatic substitution) and (2) by using the Ullman-Goldberg cross-coupling reaction to build up the acridine core, which allows for the introduction of more substituents via later nucleophilic substitution of the resultant 9-chloroacridines. I have also investigated the methylation of the aromatic acridine nitrogen to render the resulting products water-soluble and facilitate binding studies with DNA via a range of techniques, including melting point, viscosity, circular dichroism (CD), and kinetics. These studies will provide insight into how various functional groups affect the binding modes and intercalation properties of acridine derivatives
Corryn Canell, Advisor: Dr. A. Oldacre
Investigation of Azo Dye Sequestration and Electrochemical Degradation
The second largest water polluter in the world is textile industries. Of all the textile dyes used, azo dyes are the most common and have the biggest negative effect on the environment and health of humans. These toxic azo dyes are found in paints, ink, plastic, cosmetic products, and clothing items. The run-off from the industries contains azo dyes that create a thick layer covering the surface of the water, inhibiting photosynthesis from occurring. These contaminated waterbodies then run-off into water consumed by humans. The azo bond within the dye is a pre-carcinogen that, once consumed, reacts with enzymes in the liver to undergo a reduction of the dye, forming an aromatic amine. This product then undergoes further reactions in the body to form carcinogenic products. To limit the toxicity of azo dyes, it is imperative to investigate ways to remove the dyes from waterbodies and degrade using oxidative methods. Metal-organic frameworks (MOFs) are 3-dimensional porous structures that are known for their ability to sequester dyes from water. They act as micro-porous sponges to adsorb the dye, decreasing its concentration in the water. Using Lewis acid/base chemistry, we are able to facilely synthesize a variety of MOFs with a catalytic center integrated within its framework. Testing different pore-sized variations of MOFs will allow us to see that larger pore sizes are more effective and increase the rate of sequestration of the dye. Once it is sequestered, we will have efficient electrochemical degradation of azo dyes. Decreasing the amount of dye found in an isolated system and degrading the dye will allow pathways for similar experiments in larger bodies of water. Electrochemical and spectroelectrochemical experiments will be used to observe the degradation of the azo dye, methyl orange. In the electrochemistry of the environment, if there is an electron transfer there is a corresponding, facilitating proton transfer. The influence of protons on the electrochemical degradation of methyl orange will be probed using several pH solutions.
Leana Dickhens, Advisor: Dr. S. Tartakoff
Further Improvements of the Wagner-Jauregg Reaction with Tri-substituted Styrenes
Opioid compounds, such as morphine, are used as painkillers post-surgery and to manage chronic pain. Scientists have manipulated the structure of morphine forming new pain relievers but have yet to find a non-addictive molecule. The Wagner-Jauregg reaction can potentially be used to make new morphine-like molecules, with different biological properties and the possibility of less harmful side-effects. The goal of my project is to synthesize various trisubstituted styrenes, which can be reacted with existing dienophiles, such as N-methylmaleimide, to improve our understanding regarding the scope and limitations of the Wagner-Jauregg reaction. In addition, if we can make a library of morphine analogues, these compounds could be used in further research to explore less addictive painkillers.
Blake Heston, Advisor: Dr. P. Lutz
Synthesis and Analysis of Novel Self-Immolative Polymers and Copolymers
Our world today relies heavily on plastics that are hazardous for the environment in both their unsustainable production from petroleum and the negative impacts of plastic waste. Plastics are also known scientifically as polymers, long chainlike molecules made up of small molecules called monomers. Most commercial polymers cannot be efficiently degraded back to their monomers, so creating polymers that can be depolymerized would facilitate recycling and help to minimize the negative effects of plastics. Self-immolative polymers are special because they will polymerize at low temperatures when exposed to a catalyst, but they readily fragment back into the monomer if the catalyst is reintroduced at a higher temperature. The goal of this research is to identify new monomers that can be used to form self-immolative polymers with tunable physical and chemical properties. To evaluate reactivity, we will copolymerize target monomers with o-phthaladehyde (oPA), which is known to form self-immolative poly(phthalaldehyde) at temperatures below -38 ºC using cationic and anionic catalysts.
We will use NMR spectroscopy to determine the percent incorporation of each comonomer we test to determine its reactivity. For monomers that can be successfully copolymerized with oPA, we will also investigate their ability to be homopolymerized and study properties of interest of the resulting polymers (e.g., ceiling temperature, glass transition temperature, degradation). Having access to a range of degradable polymers with known and tunable properties is an important step toward incorporating self-immolative polymers into widespread applications.
Chidera Nwenyi, Advisor: Dr. A. Oldacre
Sequestering and Degrading Methyl Orange azo dye using MOF-545
Water scarcity is a type of water insecurity that describes the physical shortage of suitable water. One of the main causes of water insecurity is water pollution, in which the textile industry is the second largest industry responsible. The most predominant type of dye used in the textile industry are Azo dyes. They are water soluble compounds that have a -N=N- functionality (azo bonds) with aromatic ligands, have high resistance to biodegradation, and have mutagenic and carcinogenic properties. When the nitrogen-to-nitrogen double bond breaks during treatment of wastewater or after the dyes have been ingested, the azo bond can be reduced to aromatic amines which can be transformed into N-hydroxylamine by our liver enzymes. These compounds can damage human DNA and cause cancer. Therefore, it is imperative that we research methods of removal and safe degradation of azo dyes. A Metal-Organic Framework (MOF) is a microscopic sponge that can absorb and store materials in its pores. The "metal" refers to metal clusters or ions that serve as anchors to hold the structure together. The "organic" ligand refers to carbon-based molecules that form the structure’s framework. In this project, we will synthesize, characterize, and study the stability of MOF-545 in distilled water and acidified conditions. Then we will measure the kinetic and thermodynamic parameters of azo-dye sequestration and degradation. We hypothesize that MOF-545 will successfully sequester and degrade the azo dye, Methyl Orange.
Lydia Oikonomou, Advisor: Dr. N. Marano
Biofilm formation and amyloid protein production of four strains of bacteria isolated from water bottle filling stations.
Drinking water fountains and water bottle filling stations can be a breeding ground for bacteria that originate either from the environment or from the people that use these stations. The ability of bacteria to survive on surfaces depends on their capability to become attached to the surface of the bottle filling stations and form biofilms. Biofilms are communities of bacteria that are surrounded by an extracellular matrix which renders them resistant to disinfecting agents. This extracellular matrix can be composed of a mixture of macromolecules such as polysaccharides, proteoglycans, and amyloid proteins. The purpose of this study is to understand the kinetics of the formation of biofilms and attachment of amyloid proteins. Four bacterial strains (Acidovorax, Deinococcus, Paracoccus, Rhizobium rosettiformans) previously isolated from water bottle filling stations[1] were selected for analysis. The bacteria will be grown in R2A solid media and isolated colonies will be used to inoculate R2A liquid media. The absorbance at 600 nm will be monitored every 24 hours for 10 days in order to construct growth curves for each of the four strains. For determining biofilm formation, the crystal violet biofilm assay will be utilized. Amyloid production will be detected using the thioflavin-T assay at different time points during growth. Understanding the timing of amyloid production is important in order to deduce its role in biofilm formation.
[1] Bryne, E., Wangler G., Timerman M., Grant D., and Dean H. 2021. Identification and characterization of microbial communities in local water bottle filling stations. Biology Department, St. Lawrence University.
Emma Rothe, Advisor: Dr. P. Lutz
Synthesis of Azulene-Based Degradable Polymers
This research aims to synthesize degradable polymers based on the framework of the azulene molecule. Azulene is an aromatic hydrocarbon containing seven- and five-membered rings that result in unique chemical properties, including a significant molecular dipole not commonly found in aromatic rings. While a number of azulene-containing polymers are known, previous work has not focused on the formation of degradable materials. Our approach is to functionalize azulene derivatives with the aldehyde functional group, which we hypothesize can be polymerized to form acid-degradable polyacetals. The target monomers will be synthesized, and we will assess their reactivity under various polymerization conditions and investigate the physical and chemical properties of the resulting polymers. If successful, this research could help to increase sustainability by generating new plastics that are easily recyclable, helping to reduce the environmental impact of these materials.
Maddy Ruggiera, Advisor: Dr. S. Tartakoff
Synthesis of Novel Proflavine Derivatives as Possible DNA Binding Agents
Organic synthesis gives pharmaceutical chemists the ability to create complex molecules from cheap and readily available chemical compounds. Many of these complex organic molecules are bioactive molecules that can function as DNA intercalators— molecules that bind to DNA in a variety of modes, causing a change in the DNA. This change oftentimes results in a halt in cell function or cell death, making intercalating molecules promising chemotherapeutic agents. This project centers around creating derivatives from a known intercalating molecule, proflavine, in order to create DNA intercalators that are more soluble in water and more electrophilic, allowing for proflavine’s daughter-molecules to more effectively bind to DNA. While utilizing literature and known reactions, a small library of proflavine derivatives is being created based on the condensation of functional groups onto proflavine’s unsubstituted amines, as well as rebuilding the core acridine structure of proflavine to include reactive groups on the aromatic rings. The goal of this project is the creation of both known and novel proflavine derivatives for use in DNA and kinetics studies.
Bobby Tremont, Advisor: Dr. S. Tartakoff
The Antibiotic Pipeline Dilemma: Past Glories, Present Struggles
Antibiotics set the groundwork for modern-day drug development and synthesis, but the antibiotic drug pipeline is currently struggling to stay afloat. The problem of antibiotic resistance is ever looming, alongside the shrinking of the antibiotic pipeline. I am examining to what extent scientific, financial, and societal factors have contributed to the current landscape of the antibiotic drug pipeline. To do this, I will analyze clinical trial results/outcomes, scientific primary literature, financial statements, investor decks, and news reports. The goal is to be able to identify how influential each of these factors are, as well as what other secondary factors might be involved. This will help to pinpoint what led to the decline of the antibiotic drug pipeline and appropriate solutions can be proposed.
Brooke Westcom, Advisor: Dr. Samantha Glazier
Analysis of MIP-modified amino-Carbon Dots Synthesis for Detection of TNT
Amino-carbon dots are a type of quantum dot that is made of carbon nanomaterial and have been an effective way to detect harmful heavy metals and explosives such as 2-methyl-1,3,5-trinitrotoluene (TNT). The detection of TNT can be beneficial for safety in various settings including airports. Through fluorescence quenching, these dots help detect and determine the concentration of TNT in contaminated sources. While the carbon dots are promising, selectivity is an area of ongoing research because they are non-specific and false positives are possible due to decay products of nitrotoluene being present. A relatively new modification to be more selective in detection has been developed using molecularly imprinted polymers (MIPs). MIPs are polymers that have been synthesized around a template molecule, casting a shell around the template which leaves cavities where only targeted molecules can bind. If TNT was present in a sample, it would bind to the MIP-modified amino-carbon dot and shows change in fluorescence. The exact procedure and mechanism of the amino-carbon dot reactions have not been determined. There is some variation in reports about the effects of reaction time, temperature and dialysis on the chemical structure and associated sensitivity to TNT. We will use fluorescence and infrared spectroscopy to modify the synthesis to maximize detection efficiency and characterize the chemical structure of the product under different conditions. Once the synthesis is optimized, fluorescent titrations will be used to investigate sensitivity and selectivity of MIPs to trinitrotoluenes.